Research workbench
Crystal structure of scallop myosin S1 in the pre-power stroke state to 2.6 ångström resolution: flexibility and function in the head
Analyse Crystal structure of scallop myosin S1 in the pre-power stroke state to 2.6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QVI
- Type
- protein
- Length
- 1,102 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin heavy chain, striated muscle; Myosin regulatory light chain, striated adductor…
- UniProt
- P24733, P13543, P07291
- Ligands
- ADP, MG, CA, VO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin heavy chain, striated muscle | protein | 806 | 48% helix, 14% strand | P24733 |
| Y | Myosin regulatory light chain, striated adductor muscle | protein | 141 | 54% helix, 7% strand | P13543 |
| Z | Myosin essential light chain, striated adductor muscle | protein | 155 | 54% helix, 8% strand | P07291 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, Y
- CA · Calcium ion · metal · chains Z
- VO4 · Vanadate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.77 | 0.79 | 93 | empty |
| 2 | 603 | 0.75 | 0.82 | 70 | empty |
| 3 | 407 | 0.70 | 0.82 | 52 | MG, VO4, ADP |
| 4 | 145 | 0.49 | 0.78 | 30 | empty |
| 5 | 108 | 0.45 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–Z · 2015 Ų buried · 20 hydrogen bonds · protein-protein
- A–Y · 1887 Ų buried · 19 hydrogen bonds · protein-protein
- Y–Z · 237 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1QVI · Crystal structure of scallop myosin S1 in the pre-power stroke state to 2.6 Angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
- P07291 · AlphaFold monomer V2.0 prediction for myosin essential light chain, striated adductor… · a predicted model of the same protein · chain Z against A, TM-score 0.97
- P24733 · AlphaFold monomer V2.0 prediction for myosin heavy chain, striated muscle (P24733) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P13543 · AlphaFold monomer V2.0 prediction for myosin regulatory light chain, striated adductor… · a predicted model of the same protein · chain Y against A, TM-score 0.83
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P24733
- Every structure of UniProt P13543
- Every structure of UniProt P07291
- Elsewhere: RCSB PDB 1QVI · PDBe 1QVI · UniProt P24733 · UniProt P13543 · UniProt P07291
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